Dissecting transcription factors regulatory network to identify regulators of MAPK signaling pathway during differentiation iPSCs to primary neurosphere

Differentiation of iPSCs into neurosphere principally regulates by transcription factors (TFs). Our study focus on constructing transcription factors regulatory network and dissecting the network using system biology tools to find genesinvolve in MAPK signaling pathway and their regulators. Method:Microarray data obtained from GEO servers using GSE accession number 31598. RMA algorithm used for normalization and fold change used for detection of differential expressed (DE) genes in Flexarray environment. Threshold 3 applied for detecting DE genes. Regulatory interactions between TFs and DE genes obtained from ChEA database. Valid proteinproteininteractions identified in BioGRID database. Network ontology using ClueGO used to identify affected processesand their genes. JActiveModules Cytoscape plugin was used to detect core active subnetwork.Result: Expression profile comparison of primary neurosphere and iPSCs shows 2521 DE genes. This list contain 1413 up regulatedgenes and 1108 down regulated genes. Collectively we construct TFs regulatory network that contain 2250 DE genes with 14922 interactions. This network contains 56 DE TFs as regulators of 2235 DE genes. These TFs are involve in proteinprotein interaction network include 149 nodes and 223 edges. Network ontology based on KEGG pathway analysis reveals54 DE genes involve in MAPK signaling pathway. We identified SUZ12, POU5F1, TRP53, NANOG, STAT3, TAL1,REST, KLF4, MYC, and SALL4 as most important regulators of MAPK signaling respectively. Core active modulesanalysis show presence of 5 DE genes from MAPK signaling list in 5 top modules. Conclusion: Our result highlights the presence of MAPK signaling during iPSCs differentiation to primary neurosphere and may be help to increase efficiency of differentiation.

کلیدواژه ها:

Differentiation ، MAPK signaling ، iPSCs ، Regulatory network ، Transcription factor